Re: User-defined annotations in Stockholm alignment file
Peter Cock <[email protected]>
| Newsgroups | gmane.comp.python.bio.devel |
|---|---|
| Message-ID | <CAKVJ-_7mwh-nDXjoeK=nbYyucStwhwnHDhX_SLdT6B7h0uLxAw@mail.gmail.com> |
On Tue, Apr 5, 2016 at 8:58 AM, João Rodrigues <[email protected]> wrote: >> > My original question was why does AlignIO ignore "custom" annotations it >> > doesn't know, while writing (StockholmIO, line 254)? >> >> https://github.com/biopython/biopython/blob/master/Bio/AlignIO/StockholmIO.py#L254 >> >> Because as far as I know only a short list of accepted feature types for >> the GS lines exist (from PFAM/RFAM). The associated comment about >> this could have been prefixed with TODO - do you have a strong use >> case for custom annotations? > > Not really, just a case where I want to add my own annotations to each > sequence in an alignment. We could support "custom" annotations directly > under the keys found in the Stockholm file, instead of trying to map them > somewhere. That would keep the PFAM/RFAM keys "mappable" but extend the > format if people want to add extra things. It's a shame such an > annotation-friendly format can only take "official" annotations.. Its more I was strongly guided by PFAM as the only major user of the annotations in the Stockholm format when I wrote the Biopython code. Peter _______________________________________________ Biopython-dev mailing list [email protected] http://mailman.open-bio.org/mailman/listinfo/biopython-dev